Multiple sequence alignment - TraesCS7B01G337900

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)



BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G337900 chr7B 100.000 2749 0 0 1 2749 592535802 592533054 0.000000e+00 5077.0
1 TraesCS7B01G337900 chr7B 85.414 809 88 18 948 1751 592807927 592808710 0.000000e+00 813.0
2 TraesCS7B01G337900 chr7B 85.624 793 85 17 963 1751 592867734 592868501 0.000000e+00 806.0
3 TraesCS7B01G337900 chr7B 83.579 883 108 24 879 1755 592718413 592719264 0.000000e+00 793.0
4 TraesCS7B01G337900 chr7D 94.167 1423 56 16 541 1953 548916495 548915090 0.000000e+00 2143.0
5 TraesCS7B01G337900 chr7D 85.290 809 96 15 950 1755 549274330 549275118 0.000000e+00 813.0
6 TraesCS7B01G337900 chr7D 84.994 813 92 16 950 1755 549134791 549135580 0.000000e+00 798.0
7 TraesCS7B01G337900 chr7D 79.633 491 52 28 2295 2749 548914265 548913787 2.660000e-80 309.0
8 TraesCS7B01G337900 chr7D 82.712 295 15 19 1954 2225 548914944 548914663 2.130000e-56 230.0
9 TraesCS7B01G337900 chr7D 97.872 47 1 0 496 542 637671239 637671193 6.310000e-12 82.4
10 TraesCS7B01G337900 chr6B 95.795 547 17 4 1 542 129477391 129476846 0.000000e+00 878.0
11 TraesCS7B01G337900 chr7A 85.190 817 95 17 950 1760 634605500 634606296 0.000000e+00 815.0
12 TraesCS7B01G337900 chr7A 85.099 812 92 15 950 1755 634476928 634477716 0.000000e+00 802.0
13 TraesCS7B01G337900 chr7A 84.852 812 94 15 950 1755 634463998 634464786 0.000000e+00 791.0
14 TraesCS7B01G337900 chr7A 96.000 50 2 0 493 542 291021918 291021967 6.310000e-12 82.4
15 TraesCS7B01G337900 chr5A 93.738 543 30 4 1 542 547825330 547825869 0.000000e+00 811.0
16 TraesCS7B01G337900 chrUn 93.186 543 34 3 1 542 420212719 420212179 0.000000e+00 795.0
17 TraesCS7B01G337900 chrUn 93.002 543 35 3 1 542 379544268 379543728 0.000000e+00 789.0
18 TraesCS7B01G337900 chrUn 91.927 545 41 3 1 544 37054160 37053618 0.000000e+00 760.0
19 TraesCS7B01G337900 chr3A 95.254 295 14 0 1 295 738183693 738183987 4.150000e-128 468.0
20 TraesCS7B01G337900 chr2B 92.308 52 4 0 493 544 780580192 780580243 1.060000e-09 75.0
21 TraesCS7B01G337900 chr1A 93.333 45 3 0 493 537 44289338 44289382 1.770000e-07 67.6
22 TraesCS7B01G337900 chr3D 95.000 40 2 0 2105 2144 582052649 582052610 2.290000e-06 63.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G337900 chr7B 592533054 592535802 2748 True 5077 5077 100.000 1 2749 1 chr7B.!!$R1 2748
1 TraesCS7B01G337900 chr7B 592807927 592808710 783 False 813 813 85.414 948 1751 1 chr7B.!!$F2 803
2 TraesCS7B01G337900 chr7B 592867734 592868501 767 False 806 806 85.624 963 1751 1 chr7B.!!$F3 788
3 TraesCS7B01G337900 chr7B 592718413 592719264 851 False 793 793 83.579 879 1755 1 chr7B.!!$F1 876
4 TraesCS7B01G337900 chr7D 548913787 548916495 2708 True 894 2143 85.504 541 2749 3 chr7D.!!$R2 2208
5 TraesCS7B01G337900 chr7D 549274330 549275118 788 False 813 813 85.290 950 1755 1 chr7D.!!$F2 805
6 TraesCS7B01G337900 chr7D 549134791 549135580 789 False 798 798 84.994 950 1755 1 chr7D.!!$F1 805
7 TraesCS7B01G337900 chr6B 129476846 129477391 545 True 878 878 95.795 1 542 1 chr6B.!!$R1 541
8 TraesCS7B01G337900 chr7A 634605500 634606296 796 False 815 815 85.190 950 1760 1 chr7A.!!$F4 810
9 TraesCS7B01G337900 chr7A 634476928 634477716 788 False 802 802 85.099 950 1755 1 chr7A.!!$F3 805
10 TraesCS7B01G337900 chr7A 634463998 634464786 788 False 791 791 84.852 950 1755 1 chr7A.!!$F2 805
11 TraesCS7B01G337900 chr5A 547825330 547825869 539 False 811 811 93.738 1 542 1 chr5A.!!$F1 541
12 TraesCS7B01G337900 chrUn 420212179 420212719 540 True 795 795 93.186 1 542 1 chrUn.!!$R3 541
13 TraesCS7B01G337900 chrUn 379543728 379544268 540 True 789 789 93.002 1 542 1 chrUn.!!$R2 541
14 TraesCS7B01G337900 chrUn 37053618 37054160 542 True 760 760 91.927 1 544 1 chrUn.!!$R1 543


AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
648 660 0.038599 AGCCCATGTGCTCACAATCA 59.961 50.0 6.81 0.0 45.41 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2313 2843 0.109458 CGAGTACTAACACTGCGCCA 60.109 55.0 4.18 0.0 0.0 5.69 R


All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 0.887933 GCCAAACCACCTACCATGTG 59.112 55.000 0.00 0.00 0.00 3.21
157 158 2.050350 GTCGTCAGATCCCCACCGA 61.050 63.158 0.00 0.00 0.00 4.69
373 375 3.849574 TGGAGGTGGTTTGGATTATGAGA 59.150 43.478 0.00 0.00 0.00 3.27
464 470 0.179032 AACGTGGGATGTTGTCTGCA 60.179 50.000 0.00 0.00 0.00 4.41
502 510 1.691434 GATGACAGGAGATGGAGGTCC 59.309 57.143 0.00 0.00 0.00 4.46
582 590 3.763897 CCCTTTGGAATAGAACAACCCTG 59.236 47.826 0.00 0.00 0.00 4.45
584 592 2.507407 TGGAATAGAACAACCCTGCC 57.493 50.000 0.00 0.00 0.00 4.85
646 658 0.892755 CAAGCCCATGTGCTCACAAT 59.107 50.000 2.23 0.00 45.41 2.71
647 659 1.135199 CAAGCCCATGTGCTCACAATC 60.135 52.381 2.23 0.00 45.41 2.67
648 660 0.038599 AGCCCATGTGCTCACAATCA 59.961 50.000 6.81 0.00 45.41 2.57
649 661 0.171903 GCCCATGTGCTCACAATCAC 59.828 55.000 6.81 0.00 45.41 3.06
650 662 1.536940 CCCATGTGCTCACAATCACA 58.463 50.000 6.81 0.00 45.41 3.58
669 681 1.535462 CAAGTTGGTGAACCGTCATCC 59.465 52.381 0.00 0.00 39.43 3.51
673 685 0.535335 TGGTGAACCGTCATCCTAGC 59.465 55.000 0.00 0.00 39.43 3.42
778 790 1.321016 CTTCTTCACGCGCACATTTG 58.679 50.000 5.73 0.00 0.00 2.32
779 791 0.660488 TTCTTCACGCGCACATTTGT 59.340 45.000 5.73 0.00 0.00 2.83
789 801 2.161410 GCGCACATTTGTATCTGTTCCA 59.839 45.455 0.30 0.00 0.00 3.53
831 843 3.844577 ATCATCAAGCACAAGCAGAAC 57.155 42.857 0.00 0.00 45.49 3.01
838 850 0.169672 GCACAAGCAGAACATCGCAT 59.830 50.000 0.00 0.00 41.58 4.73
861 873 7.201418 GCATTGATCTGATACGATATCACACAG 60.201 40.741 3.12 6.68 0.00 3.66
862 874 5.703876 TGATCTGATACGATATCACACAGC 58.296 41.667 3.12 0.00 0.00 4.40
863 875 4.147219 TCTGATACGATATCACACAGCG 57.853 45.455 3.12 0.00 0.00 5.18
873 885 4.778415 ACACAGCGCGCCTACTCG 62.778 66.667 30.33 13.17 0.00 4.18
909 921 1.265905 GCTCCCAATAATTTACCCGCG 59.734 52.381 0.00 0.00 0.00 6.46
928 940 5.530171 CCCGCGTGATACTACCAGTATATAT 59.470 44.000 4.92 0.00 41.21 0.86
929 941 6.707608 CCCGCGTGATACTACCAGTATATATA 59.292 42.308 4.92 0.00 41.21 0.86
961 977 0.688487 TACCTTACCTGCAGCCGTTT 59.312 50.000 8.66 0.00 0.00 3.60
1080 1097 2.588439 GCCTTCGACCCTAACCCC 59.412 66.667 0.00 0.00 0.00 4.95
1147 1165 2.109609 TAAACGCCGTGCTAGTATCG 57.890 50.000 0.00 0.00 0.00 2.92
1163 1193 6.692249 GCTAGTATCGACTCTTTGGTTTCTAC 59.308 42.308 0.00 0.00 37.10 2.59
1166 1196 5.633830 ATCGACTCTTTGGTTTCTACGTA 57.366 39.130 0.00 0.00 0.00 3.57
1167 1197 4.787598 TCGACTCTTTGGTTTCTACGTAC 58.212 43.478 0.00 0.00 0.00 3.67
1169 1199 5.009010 TCGACTCTTTGGTTTCTACGTACTT 59.991 40.000 0.00 0.00 0.00 2.24
1170 1200 5.341727 CGACTCTTTGGTTTCTACGTACTTC 59.658 44.000 0.00 0.00 0.00 3.01
1171 1201 5.218139 ACTCTTTGGTTTCTACGTACTTCG 58.782 41.667 0.00 0.00 46.00 3.79
1172 1202 5.009010 ACTCTTTGGTTTCTACGTACTTCGA 59.991 40.000 0.00 0.00 42.86 3.71
1173 1203 5.830912 TCTTTGGTTTCTACGTACTTCGAA 58.169 37.500 0.00 0.00 42.86 3.71
1174 1204 6.272318 TCTTTGGTTTCTACGTACTTCGAAA 58.728 36.000 0.00 4.19 42.86 3.46
1175 1205 6.925165 TCTTTGGTTTCTACGTACTTCGAAAT 59.075 34.615 9.95 0.00 42.86 2.17
1176 1206 6.456447 TTGGTTTCTACGTACTTCGAAATG 57.544 37.500 9.95 0.00 42.86 2.32
1177 1207 5.531634 TGGTTTCTACGTACTTCGAAATGT 58.468 37.500 9.95 0.00 42.86 2.71
1182 1212 5.260900 TCTACGTACTTCGAAATGTGATCG 58.739 41.667 0.00 5.02 42.86 3.69
1188 1218 4.748892 ACTTCGAAATGTGATCGTCATCT 58.251 39.130 0.00 0.00 40.99 2.90
1195 1225 3.733443 TGTGATCGTCATCTATGGTGG 57.267 47.619 0.00 0.00 0.00 4.61
1196 1226 2.224042 TGTGATCGTCATCTATGGTGGC 60.224 50.000 0.00 0.00 0.00 5.01
1199 1229 3.831911 TGATCGTCATCTATGGTGGCATA 59.168 43.478 0.00 0.00 0.00 3.14
1699 1734 1.469940 CGTTGCTAAGTCGCTCCTCAT 60.470 52.381 0.00 0.00 0.00 2.90
1703 1738 1.342819 GCTAAGTCGCTCCTCATGGAT 59.657 52.381 0.00 0.00 42.29 3.41
1760 1795 1.396607 GGCCTTGATGCATGCATGGA 61.397 55.000 36.73 25.66 36.70 3.41
1773 1808 0.391130 GCATGGACACGCTGTTCCTA 60.391 55.000 0.00 0.00 0.00 2.94
1778 1813 1.202428 GGACACGCTGTTCCTATCTCC 60.202 57.143 0.00 0.00 0.00 3.71
1779 1814 1.751924 GACACGCTGTTCCTATCTCCT 59.248 52.381 0.00 0.00 0.00 3.69
1802 1837 0.168128 GTATTGTCTGCGGGCACAAC 59.832 55.000 0.00 0.00 35.37 3.32
1817 1852 2.285544 GCACAACAATTTGCAACCGTTC 60.286 45.455 0.00 0.00 38.68 3.95
1831 1866 4.143137 GCAACCGTTCCTTTGCAATAAATG 60.143 41.667 0.00 0.76 46.13 2.32
1904 1939 1.592400 TTCGCTCTGTACCTCCCACG 61.592 60.000 0.00 0.00 0.00 4.94
1953 1988 5.392767 TTGACTGTCACTGGTCTAGAATC 57.607 43.478 10.56 0.00 34.01 2.52
1954 1989 4.407365 TGACTGTCACTGGTCTAGAATCA 58.593 43.478 6.36 0.00 34.01 2.57
1955 1990 4.832823 TGACTGTCACTGGTCTAGAATCAA 59.167 41.667 6.36 0.00 34.01 2.57
1956 1991 5.047731 TGACTGTCACTGGTCTAGAATCAAG 60.048 44.000 6.36 0.00 34.01 3.02
1957 1992 5.080337 ACTGTCACTGGTCTAGAATCAAGA 58.920 41.667 0.00 0.00 0.00 3.02
1958 1993 5.184864 ACTGTCACTGGTCTAGAATCAAGAG 59.815 44.000 0.00 0.00 0.00 2.85
1959 1994 5.080337 TGTCACTGGTCTAGAATCAAGAGT 58.920 41.667 0.00 0.00 0.00 3.24
2003 2182 1.346068 GGCTATCCATTCCTCGAGCTT 59.654 52.381 6.99 0.00 0.00 3.74
2006 2185 4.503296 GGCTATCCATTCCTCGAGCTTTAA 60.503 45.833 6.99 0.00 0.00 1.52
2012 2191 4.095036 CCATTCCTCGAGCTTTAAACCTTC 59.905 45.833 6.99 0.00 0.00 3.46
2015 2194 3.833070 TCCTCGAGCTTTAAACCTTCTCT 59.167 43.478 6.99 0.00 0.00 3.10
2019 2198 3.611970 GAGCTTTAAACCTTCTCTCCCC 58.388 50.000 0.00 0.00 0.00 4.81
2056 2235 1.959508 GCTGCTTCCTCTCCTCTCTGA 60.960 57.143 0.00 0.00 0.00 3.27
2065 2244 3.432588 CCTCTCTGACGGTCGCGT 61.433 66.667 5.77 0.00 0.00 6.01
2146 2348 3.716006 CGCAAGCTGGTGACCACG 61.716 66.667 0.00 0.00 0.00 4.94
2147 2349 2.280797 GCAAGCTGGTGACCACGA 60.281 61.111 0.00 0.00 0.00 4.35
2148 2350 2.320587 GCAAGCTGGTGACCACGAG 61.321 63.158 0.00 7.65 39.70 4.18
2149 2351 1.069765 CAAGCTGGTGACCACGAGT 59.930 57.895 0.00 0.00 39.05 4.18
2150 2352 0.946221 CAAGCTGGTGACCACGAGTC 60.946 60.000 0.00 0.00 46.51 3.36
2151 2353 2.048127 GCTGGTGACCACGAGTCC 60.048 66.667 0.00 0.00 45.68 3.85
2152 2354 2.867855 GCTGGTGACCACGAGTCCA 61.868 63.158 0.00 0.70 45.68 4.02
2153 2355 1.006102 CTGGTGACCACGAGTCCAC 60.006 63.158 0.00 0.00 45.68 4.02
2154 2356 2.049433 GGTGACCACGAGTCCACG 60.049 66.667 0.00 0.00 45.68 4.94
2167 2369 1.450134 TCCACGACCTGCATGCATC 60.450 57.895 22.97 16.00 0.00 3.91
2168 2370 1.746239 CCACGACCTGCATGCATCA 60.746 57.895 22.97 0.00 0.00 3.07
2169 2371 1.712018 CCACGACCTGCATGCATCAG 61.712 60.000 22.97 15.40 0.00 2.90
2198 2400 2.352225 GGATCGATTCTCTCCGTGATGG 60.352 54.545 0.00 0.00 40.09 3.51
2225 2427 1.143684 ACGATGGGAGGAATCCAATGG 59.856 52.381 0.61 0.00 37.87 3.16
2226 2428 1.421268 CGATGGGAGGAATCCAATGGA 59.579 52.381 3.67 3.67 37.87 3.41
2227 2429 2.551721 CGATGGGAGGAATCCAATGGAG 60.552 54.545 8.40 0.00 37.87 3.86
2228 2430 1.985622 TGGGAGGAATCCAATGGAGT 58.014 50.000 8.40 4.62 34.05 3.85
2229 2431 1.565759 TGGGAGGAATCCAATGGAGTG 59.434 52.381 7.08 0.00 34.05 3.51
2230 2432 1.685148 GGAGGAATCCAATGGAGTGC 58.315 55.000 13.33 13.33 38.37 4.40
2232 2434 2.725221 AGGAATCCAATGGAGTGCTC 57.275 50.000 17.82 6.44 44.56 4.26
2233 2435 2.203584 AGGAATCCAATGGAGTGCTCT 58.796 47.619 17.82 4.66 44.56 4.09
2234 2436 2.172293 AGGAATCCAATGGAGTGCTCTC 59.828 50.000 17.82 7.26 44.56 3.20
2235 2437 2.172293 GGAATCCAATGGAGTGCTCTCT 59.828 50.000 13.90 0.00 35.36 3.10
2236 2438 3.465871 GAATCCAATGGAGTGCTCTCTC 58.534 50.000 7.08 6.54 40.29 3.20
2239 2441 1.134461 CCAATGGAGTGCTCTCTCAGG 60.134 57.143 14.98 8.68 40.29 3.86
2240 2442 1.134461 CAATGGAGTGCTCTCTCAGGG 60.134 57.143 14.98 5.15 40.29 4.45
2241 2443 1.336632 ATGGAGTGCTCTCTCAGGGC 61.337 60.000 14.98 0.00 40.29 5.19
2243 2445 0.396417 GGAGTGCTCTCTCAGGGCTA 60.396 60.000 14.98 0.00 40.29 3.93
2246 2448 0.179086 GTGCTCTCTCAGGGCTAAGC 60.179 60.000 0.00 0.00 0.00 3.09
2263 2757 5.224135 GCTAAGCCTGCTAGTAGATGTTAC 58.776 45.833 9.72 0.00 0.00 2.50
2287 2781 1.956477 GTTGCATGGTTGGACTCTTGT 59.044 47.619 0.00 0.00 0.00 3.16
2292 2786 3.415212 CATGGTTGGACTCTTGTGATGT 58.585 45.455 0.00 0.00 0.00 3.06
2293 2787 3.576078 TGGTTGGACTCTTGTGATGTT 57.424 42.857 0.00 0.00 0.00 2.71
2311 2841 2.168313 TGTTAGCTTGATGATCGAGGCA 59.832 45.455 11.48 0.00 0.00 4.75
2312 2842 2.799412 GTTAGCTTGATGATCGAGGCAG 59.201 50.000 11.48 0.00 0.00 4.85
2313 2843 0.829333 AGCTTGATGATCGAGGCAGT 59.171 50.000 11.48 0.00 0.00 4.40
2315 2845 1.579698 CTTGATGATCGAGGCAGTGG 58.420 55.000 1.54 0.00 0.00 4.00
2316 2846 0.462581 TTGATGATCGAGGCAGTGGC 60.463 55.000 9.02 9.02 40.13 5.01
2318 2848 4.819761 TGATCGAGGCAGTGGCGC 62.820 66.667 11.51 11.00 42.47 6.53
2323 2853 4.996434 GAGGCAGTGGCGCAGTGT 62.996 66.667 15.57 0.00 42.47 3.55
2324 2854 4.569180 AGGCAGTGGCGCAGTGTT 62.569 61.111 10.83 0.00 42.47 3.32
2325 2855 2.668212 GGCAGTGGCGCAGTGTTA 60.668 61.111 10.83 0.00 42.47 2.41
2326 2856 2.680913 GGCAGTGGCGCAGTGTTAG 61.681 63.158 10.83 0.00 42.47 2.34
2327 2857 1.961277 GCAGTGGCGCAGTGTTAGT 60.961 57.895 10.83 0.00 37.16 2.24
2328 2858 0.669318 GCAGTGGCGCAGTGTTAGTA 60.669 55.000 10.83 0.00 37.16 1.82
2329 2859 1.068474 CAGTGGCGCAGTGTTAGTAC 58.932 55.000 10.83 0.00 30.89 2.73
2330 2860 0.966920 AGTGGCGCAGTGTTAGTACT 59.033 50.000 10.83 0.00 0.00 2.73
2331 2861 1.067776 AGTGGCGCAGTGTTAGTACTC 60.068 52.381 10.83 0.00 0.00 2.59
2334 2864 1.202268 GGCGCAGTGTTAGTACTCGAT 60.202 52.381 10.83 0.00 0.00 3.59
2337 2867 2.846550 CGCAGTGTTAGTACTCGATGTG 59.153 50.000 0.00 0.00 0.00 3.21
2338 2868 3.179830 GCAGTGTTAGTACTCGATGTGG 58.820 50.000 0.00 0.00 0.00 4.17
2339 2869 3.367087 GCAGTGTTAGTACTCGATGTGGT 60.367 47.826 0.00 0.00 0.00 4.16
2340 2870 4.142534 GCAGTGTTAGTACTCGATGTGGTA 60.143 45.833 0.00 0.00 0.00 3.25
2341 2871 5.570344 CAGTGTTAGTACTCGATGTGGTAG 58.430 45.833 0.00 0.00 0.00 3.18
2342 2872 5.353400 CAGTGTTAGTACTCGATGTGGTAGA 59.647 44.000 0.00 0.00 0.00 2.59
2351 2881 1.405526 CGATGTGGTAGAGTTGGTGGG 60.406 57.143 0.00 0.00 0.00 4.61
2352 2882 1.906574 GATGTGGTAGAGTTGGTGGGA 59.093 52.381 0.00 0.00 0.00 4.37
2354 2884 0.613777 GTGGTAGAGTTGGTGGGAGG 59.386 60.000 0.00 0.00 0.00 4.30
2355 2885 0.490017 TGGTAGAGTTGGTGGGAGGA 59.510 55.000 0.00 0.00 0.00 3.71
2357 2887 1.486726 GGTAGAGTTGGTGGGAGGATG 59.513 57.143 0.00 0.00 0.00 3.51
2359 2889 2.277008 AGAGTTGGTGGGAGGATGAT 57.723 50.000 0.00 0.00 0.00 2.45
2373 2903 1.134818 GGATGATATGTATCGCCCGCA 60.135 52.381 0.00 0.00 35.48 5.69
2374 2904 2.196749 GATGATATGTATCGCCCGCAG 58.803 52.381 0.00 0.00 35.48 5.18
2375 2905 0.389817 TGATATGTATCGCCCGCAGC 60.390 55.000 0.00 0.00 35.48 5.25
2384 2914 3.127533 GCCCGCAGCGTTCTTGAT 61.128 61.111 15.05 0.00 0.00 2.57
2386 2916 1.741401 CCCGCAGCGTTCTTGATCA 60.741 57.895 15.05 0.00 0.00 2.92
2426 2960 3.760035 CCGGCTAGCGTGGAGTGT 61.760 66.667 17.37 0.00 0.00 3.55
2440 2974 1.668419 GAGTGTGCCGGCAGAATATT 58.332 50.000 33.73 15.20 0.00 1.28
2444 2978 1.295792 GTGCCGGCAGAATATTTCGA 58.704 50.000 33.73 0.00 34.02 3.71
2447 2981 2.290367 TGCCGGCAGAATATTTCGAATG 59.710 45.455 29.03 0.00 34.02 2.67
2454 2988 5.106908 GGCAGAATATTTCGAATGGCTAGAC 60.107 44.000 12.04 0.00 34.02 2.59
2455 2989 5.466728 GCAGAATATTTCGAATGGCTAGACA 59.533 40.000 0.00 0.00 34.02 3.41
2456 2990 6.347240 GCAGAATATTTCGAATGGCTAGACAG 60.347 42.308 3.72 0.00 34.02 3.51
2465 2999 4.335874 CGAATGGCTAGACAGTACTACAGT 59.664 45.833 3.72 0.00 0.00 3.55
2469 3003 3.565063 GGCTAGACAGTACTACAGTAGCC 59.435 52.174 20.49 20.49 33.98 3.93
2478 3012 5.236047 CAGTACTACAGTAGCCTAGTTACGG 59.764 48.000 7.57 0.00 0.00 4.02
2481 3015 5.012893 ACTACAGTAGCCTAGTTACGGTTT 58.987 41.667 7.57 0.71 31.72 3.27
2489 3023 3.316029 GCCTAGTTACGGTTTGTGGTTTT 59.684 43.478 0.00 0.00 0.00 2.43
2501 3035 6.073494 CGGTTTGTGGTTTTTCTTTCTGTTTT 60.073 34.615 0.00 0.00 0.00 2.43
2532 3073 7.835634 TTAATTTTCCACTTCACCACAAAAC 57.164 32.000 0.00 0.00 0.00 2.43
2535 3076 2.096248 TCCACTTCACCACAAAACACC 58.904 47.619 0.00 0.00 0.00 4.16
2555 3096 7.206981 ACACCTTTCATACAACAATTGAGAG 57.793 36.000 13.59 3.78 0.00 3.20
2558 3099 7.805071 CACCTTTCATACAACAATTGAGAGTTC 59.195 37.037 13.59 0.00 0.00 3.01
2559 3100 7.502226 ACCTTTCATACAACAATTGAGAGTTCA 59.498 33.333 13.59 0.00 0.00 3.18
2561 3102 9.734620 CTTTCATACAACAATTGAGAGTTCAAA 57.265 29.630 13.59 3.05 45.82 2.69
2746 3310 8.891720 AGTAACACAATGAACAATTTGCAATTT 58.108 25.926 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
157 158 1.342819 GGAGCGAGGACATGCTTAGAT 59.657 52.381 0.00 0.00 42.60 1.98
295 296 2.283894 TCGGCTCCTGCTTCCTCA 60.284 61.111 0.00 0.00 39.59 3.86
341 343 0.325671 ACCACCTCCATGTCGATCCT 60.326 55.000 0.00 0.00 0.00 3.24
373 375 3.492353 CTCCCACGCCCCCATCAT 61.492 66.667 0.00 0.00 0.00 2.45
502 510 3.186409 AGAATTGAACGTCGTGATGGTTG 59.814 43.478 0.00 0.00 0.00 3.77
582 590 0.895100 TGGGAGCAGTTGATTGTGGC 60.895 55.000 0.00 0.00 0.00 5.01
584 592 1.538512 CAGTGGGAGCAGTTGATTGTG 59.461 52.381 0.00 0.00 0.00 3.33
646 658 1.066071 TGACGGTTCACCAACTTGTGA 60.066 47.619 0.00 0.00 43.26 3.58
647 659 1.374560 TGACGGTTCACCAACTTGTG 58.625 50.000 0.00 0.00 37.59 3.33
648 660 2.218603 GATGACGGTTCACCAACTTGT 58.781 47.619 0.00 0.00 33.38 3.16
649 661 1.535462 GGATGACGGTTCACCAACTTG 59.465 52.381 0.00 0.00 33.38 3.16
650 662 1.420138 AGGATGACGGTTCACCAACTT 59.580 47.619 0.00 0.00 33.38 2.66
661 673 3.616721 CGGGGGCTAGGATGACGG 61.617 72.222 0.00 0.00 0.00 4.79
740 752 3.576078 AGGATTCGATGCAACCCATTA 57.424 42.857 0.00 0.00 33.29 1.90
831 843 6.694411 TGATATCGTATCAGATCAATGCGATG 59.306 38.462 28.00 6.87 46.59 3.84
838 850 6.152379 GCTGTGTGATATCGTATCAGATCAA 58.848 40.000 15.89 0.00 30.43 2.57
861 873 2.938539 ATGAGTTCGAGTAGGCGCGC 62.939 60.000 25.94 25.94 37.81 6.86
862 874 0.525668 AATGAGTTCGAGTAGGCGCG 60.526 55.000 0.00 0.00 39.25 6.86
863 875 1.201343 GAATGAGTTCGAGTAGGCGC 58.799 55.000 0.00 0.00 0.00 6.53
873 885 2.098770 GGGAGCTTGCATGAATGAGTTC 59.901 50.000 3.33 0.00 34.85 3.01
928 940 7.293299 TGCAGGTAAGGTAGGAGTAGTAGTATA 59.707 40.741 0.00 0.00 0.00 1.47
929 941 6.102321 TGCAGGTAAGGTAGGAGTAGTAGTAT 59.898 42.308 0.00 0.00 0.00 2.12
941 953 0.249398 AACGGCTGCAGGTAAGGTAG 59.751 55.000 17.12 0.00 0.00 3.18
947 959 1.192146 AGGAGAAACGGCTGCAGGTA 61.192 55.000 17.12 0.00 0.00 3.08
1080 1097 1.216710 GACGCAGAAGTCCTGGAGG 59.783 63.158 0.00 0.00 43.13 4.30
1147 1165 5.341727 CGAAGTACGTAGAAACCAAAGAGTC 59.658 44.000 0.00 0.00 37.22 3.36
1163 1193 3.849708 TGACGATCACATTTCGAAGTACG 59.150 43.478 0.00 4.16 39.81 3.67
1166 1196 4.748892 AGATGACGATCACATTTCGAAGT 58.251 39.130 0.00 0.00 39.81 3.01
1167 1197 6.128982 CCATAGATGACGATCACATTTCGAAG 60.129 42.308 0.00 0.00 39.81 3.79
1169 1199 5.221244 ACCATAGATGACGATCACATTTCGA 60.221 40.000 0.00 0.00 39.81 3.71
1170 1200 4.984785 ACCATAGATGACGATCACATTTCG 59.015 41.667 0.00 0.00 42.20 3.46
1171 1201 5.178252 CCACCATAGATGACGATCACATTTC 59.822 44.000 0.00 0.00 0.00 2.17
1172 1202 5.059161 CCACCATAGATGACGATCACATTT 58.941 41.667 0.00 2.18 0.00 2.32
1173 1203 4.635223 CCACCATAGATGACGATCACATT 58.365 43.478 0.00 0.00 0.00 2.71
1174 1204 3.555795 GCCACCATAGATGACGATCACAT 60.556 47.826 0.00 2.63 0.00 3.21
1175 1205 2.224042 GCCACCATAGATGACGATCACA 60.224 50.000 0.00 0.00 0.00 3.58
1176 1206 2.224042 TGCCACCATAGATGACGATCAC 60.224 50.000 0.00 0.00 0.00 3.06
1177 1207 2.038659 TGCCACCATAGATGACGATCA 58.961 47.619 0.00 0.00 0.00 2.92
1182 1212 2.069273 GCGTATGCCACCATAGATGAC 58.931 52.381 0.00 0.00 34.72 3.06
1188 1218 1.885388 GCACGCGTATGCCACCATA 60.885 57.895 13.44 0.00 39.86 2.74
1314 1349 3.751246 CGCCGAGAACCCGTACCA 61.751 66.667 0.00 0.00 0.00 3.25
1547 1582 4.335647 AAGTGCACGAGCCCCTGG 62.336 66.667 12.01 0.00 41.13 4.45
1595 1630 1.365633 GCTGAGGGAGGCGTAGATG 59.634 63.158 0.00 0.00 0.00 2.90
1682 1717 0.461548 CCATGAGGAGCGACTTAGCA 59.538 55.000 0.00 0.00 40.15 3.49
1699 1734 2.717044 CCGACGGTGTGCCTATCCA 61.717 63.158 5.48 0.00 0.00 3.41
1703 1738 3.066190 CTCCCGACGGTGTGCCTA 61.066 66.667 13.94 0.00 0.00 3.93
1760 1795 1.751924 GAGGAGATAGGAACAGCGTGT 59.248 52.381 0.00 0.00 0.00 4.49
1773 1808 2.363680 CGCAGACAATACAGGAGGAGAT 59.636 50.000 0.00 0.00 0.00 2.75
1778 1813 0.811616 GCCCGCAGACAATACAGGAG 60.812 60.000 0.00 0.00 0.00 3.69
1779 1814 1.220749 GCCCGCAGACAATACAGGA 59.779 57.895 0.00 0.00 0.00 3.86
1802 1837 3.857923 CAAAGGAACGGTTGCAAATTG 57.142 42.857 14.88 11.84 0.00 2.32
1817 1852 5.005012 CGCAGATGTTCATTTATTGCAAAGG 59.995 40.000 1.71 0.00 0.00 3.11
1831 1866 1.267732 CGAAATCCAGCGCAGATGTTC 60.268 52.381 11.47 15.02 45.74 3.18
1904 1939 4.750460 TCACAAGGAGACACACGC 57.250 55.556 0.00 0.00 0.00 5.34
1953 1988 5.920273 GTCTCTCTTCAGTCTTGAACTCTTG 59.080 44.000 0.00 0.00 38.37 3.02
1954 1989 5.278266 CGTCTCTCTTCAGTCTTGAACTCTT 60.278 44.000 0.00 0.00 38.37 2.85
1955 1990 4.215399 CGTCTCTCTTCAGTCTTGAACTCT 59.785 45.833 0.00 0.00 38.37 3.24
1956 1991 4.472286 CGTCTCTCTTCAGTCTTGAACTC 58.528 47.826 0.00 0.00 38.37 3.01
1957 1992 3.254657 CCGTCTCTCTTCAGTCTTGAACT 59.745 47.826 0.00 0.00 38.37 3.01
1958 1993 3.253677 TCCGTCTCTCTTCAGTCTTGAAC 59.746 47.826 0.00 0.00 38.37 3.18
1959 1994 3.253677 GTCCGTCTCTCTTCAGTCTTGAA 59.746 47.826 0.00 0.00 40.92 2.69
2003 2182 0.616891 GCCGGGGAGAGAAGGTTTAA 59.383 55.000 2.18 0.00 0.00 1.52
2006 2185 3.009714 GGCCGGGGAGAGAAGGTT 61.010 66.667 2.18 0.00 0.00 3.50
2012 2191 3.470888 ATTGACGGCCGGGGAGAG 61.471 66.667 31.76 0.00 0.00 3.20
2015 2194 4.402528 CACATTGACGGCCGGGGA 62.403 66.667 31.76 14.83 0.00 4.81
2065 2244 1.019805 TGCAACGTTTGTGTCCACGA 61.020 50.000 0.00 0.00 39.76 4.35
2142 2344 2.258591 CAGGTCGTGGACTCGTGG 59.741 66.667 0.00 0.00 32.47 4.94
2146 2348 2.103042 GCATGCAGGTCGTGGACTC 61.103 63.158 14.21 0.00 32.47 3.36
2147 2349 2.046892 GCATGCAGGTCGTGGACT 60.047 61.111 14.21 0.00 32.47 3.85
2148 2350 1.709147 GATGCATGCAGGTCGTGGAC 61.709 60.000 26.69 4.96 34.79 4.02
2149 2351 1.450134 GATGCATGCAGGTCGTGGA 60.450 57.895 26.69 0.00 36.45 4.02
2150 2352 1.712018 CTGATGCATGCAGGTCGTGG 61.712 60.000 26.69 9.82 32.31 4.94
2151 2353 1.719709 CTGATGCATGCAGGTCGTG 59.280 57.895 26.69 12.16 34.80 4.35
2152 2354 2.110967 GCTGATGCATGCAGGTCGT 61.111 57.895 26.69 8.70 39.41 4.34
2153 2355 2.110352 TGCTGATGCATGCAGGTCG 61.110 57.895 26.69 15.47 45.31 4.79
2154 2356 3.914094 TGCTGATGCATGCAGGTC 58.086 55.556 26.69 19.50 45.31 3.85
2167 2369 1.617850 AGAATCGATCCCTAGCTGCTG 59.382 52.381 13.43 2.21 0.00 4.41
2168 2370 1.892474 GAGAATCGATCCCTAGCTGCT 59.108 52.381 7.57 7.57 0.00 4.24
2169 2371 1.892474 AGAGAATCGATCCCTAGCTGC 59.108 52.381 0.00 0.00 42.67 5.25
2178 2380 2.554462 TCCATCACGGAGAGAATCGATC 59.446 50.000 0.00 0.00 39.64 3.69
2198 2400 3.594134 GATTCCTCCCATCGTGATCATC 58.406 50.000 0.00 0.00 0.00 2.92
2209 2411 1.565759 CACTCCATTGGATTCCTCCCA 59.434 52.381 5.70 0.00 41.29 4.37
2225 2427 1.408702 CTTAGCCCTGAGAGAGCACTC 59.591 57.143 2.51 2.51 42.90 3.51
2226 2428 1.484038 CTTAGCCCTGAGAGAGCACT 58.516 55.000 0.00 0.00 0.00 4.40
2227 2429 0.179086 GCTTAGCCCTGAGAGAGCAC 60.179 60.000 0.00 0.00 0.00 4.40
2228 2430 1.333636 GGCTTAGCCCTGAGAGAGCA 61.334 60.000 13.12 0.00 44.06 4.26
2229 2431 1.445518 GGCTTAGCCCTGAGAGAGC 59.554 63.158 13.12 0.00 44.06 4.09
2240 2442 4.329462 AACATCTACTAGCAGGCTTAGC 57.671 45.455 0.00 0.00 0.00 3.09
2241 2443 5.536916 AGGTAACATCTACTAGCAGGCTTAG 59.463 44.000 0.00 0.00 41.41 2.18
2243 2445 4.290942 AGGTAACATCTACTAGCAGGCTT 58.709 43.478 0.00 0.00 41.41 4.35
2246 2448 5.599999 ACAAGGTAACATCTACTAGCAGG 57.400 43.478 0.00 0.00 41.41 4.85
2247 2449 5.292101 GCAACAAGGTAACATCTACTAGCAG 59.708 44.000 0.00 0.00 41.41 4.24
2248 2450 5.175859 GCAACAAGGTAACATCTACTAGCA 58.824 41.667 0.00 0.00 41.41 3.49
2249 2451 5.175859 TGCAACAAGGTAACATCTACTAGC 58.824 41.667 0.00 0.00 41.41 3.42
2250 2452 6.258727 CCATGCAACAAGGTAACATCTACTAG 59.741 42.308 0.00 0.00 41.41 2.57
2251 2453 6.112734 CCATGCAACAAGGTAACATCTACTA 58.887 40.000 0.00 0.00 41.41 1.82
2252 2454 4.943705 CCATGCAACAAGGTAACATCTACT 59.056 41.667 0.00 0.00 41.41 2.57
2253 2455 4.700213 ACCATGCAACAAGGTAACATCTAC 59.300 41.667 0.00 0.00 33.45 2.59
2254 2456 4.917385 ACCATGCAACAAGGTAACATCTA 58.083 39.130 0.00 0.00 33.45 1.98
2256 2458 4.236935 CAACCATGCAACAAGGTAACATC 58.763 43.478 0.00 0.00 34.15 3.06
2257 2459 3.006752 CCAACCATGCAACAAGGTAACAT 59.993 43.478 0.00 0.00 34.15 2.71
2258 2460 2.363680 CCAACCATGCAACAAGGTAACA 59.636 45.455 0.00 0.00 34.15 2.41
2263 2757 1.270550 GAGTCCAACCATGCAACAAGG 59.729 52.381 0.00 0.00 0.00 3.61
2287 2781 4.625028 CCTCGATCATCAAGCTAACATCA 58.375 43.478 0.00 0.00 0.00 3.07
2292 2786 2.432146 ACTGCCTCGATCATCAAGCTAA 59.568 45.455 0.00 0.00 0.00 3.09
2293 2787 2.034878 ACTGCCTCGATCATCAAGCTA 58.965 47.619 0.00 0.00 0.00 3.32
2311 2841 0.966920 AGTACTAACACTGCGCCACT 59.033 50.000 4.18 0.00 0.00 4.00
2312 2842 1.347320 GAGTACTAACACTGCGCCAC 58.653 55.000 4.18 0.00 0.00 5.01
2313 2843 0.109458 CGAGTACTAACACTGCGCCA 60.109 55.000 4.18 0.00 0.00 5.69
2315 2845 1.846782 CATCGAGTACTAACACTGCGC 59.153 52.381 0.00 0.00 0.00 6.09
2316 2846 2.846550 CACATCGAGTACTAACACTGCG 59.153 50.000 0.00 0.00 0.00 5.18
2318 2848 4.436242 ACCACATCGAGTACTAACACTG 57.564 45.455 0.00 0.00 0.00 3.66
2323 2853 5.356190 CCAACTCTACCACATCGAGTACTAA 59.644 44.000 0.00 0.00 37.04 2.24
2324 2854 4.880120 CCAACTCTACCACATCGAGTACTA 59.120 45.833 0.00 0.00 37.04 1.82
2325 2855 3.695060 CCAACTCTACCACATCGAGTACT 59.305 47.826 0.00 0.00 37.04 2.73
2326 2856 3.442977 ACCAACTCTACCACATCGAGTAC 59.557 47.826 0.00 0.00 37.04 2.73
2327 2857 3.442625 CACCAACTCTACCACATCGAGTA 59.557 47.826 0.00 0.00 37.04 2.59
2328 2858 2.231478 CACCAACTCTACCACATCGAGT 59.769 50.000 0.00 0.00 39.53 4.18
2329 2859 2.417379 CCACCAACTCTACCACATCGAG 60.417 54.545 0.00 0.00 0.00 4.04
2330 2860 1.548719 CCACCAACTCTACCACATCGA 59.451 52.381 0.00 0.00 0.00 3.59
2331 2861 1.405526 CCCACCAACTCTACCACATCG 60.406 57.143 0.00 0.00 0.00 3.84
2334 2864 1.348064 CTCCCACCAACTCTACCACA 58.652 55.000 0.00 0.00 0.00 4.17
2337 2867 1.486726 CATCCTCCCACCAACTCTACC 59.513 57.143 0.00 0.00 0.00 3.18
2338 2868 2.467880 TCATCCTCCCACCAACTCTAC 58.532 52.381 0.00 0.00 0.00 2.59
2339 2869 2.940514 TCATCCTCCCACCAACTCTA 57.059 50.000 0.00 0.00 0.00 2.43
2340 2870 2.277008 ATCATCCTCCCACCAACTCT 57.723 50.000 0.00 0.00 0.00 3.24
2341 2871 3.392616 ACATATCATCCTCCCACCAACTC 59.607 47.826 0.00 0.00 0.00 3.01
2342 2872 3.397527 ACATATCATCCTCCCACCAACT 58.602 45.455 0.00 0.00 0.00 3.16
2351 2881 2.799917 GCGGGCGATACATATCATCCTC 60.800 54.545 0.00 0.00 32.98 3.71
2352 2882 1.137086 GCGGGCGATACATATCATCCT 59.863 52.381 0.00 0.00 32.98 3.24
2354 2884 2.196749 CTGCGGGCGATACATATCATC 58.803 52.381 0.00 0.00 32.98 2.92
2355 2885 1.740380 GCTGCGGGCGATACATATCAT 60.740 52.381 0.00 0.00 32.98 2.45
2357 2887 2.373938 GCTGCGGGCGATACATATC 58.626 57.895 0.00 0.00 0.00 1.63
2373 2903 1.929836 GATCGCTTGATCAAGAACGCT 59.070 47.619 34.43 21.72 46.42 5.07
2374 2904 2.359523 GATCGCTTGATCAAGAACGC 57.640 50.000 34.43 20.75 46.42 4.84
2426 2960 2.031258 TTCGAAATATTCTGCCGGCA 57.969 45.000 30.59 30.59 0.00 5.69
2440 2974 4.945543 TGTAGTACTGTCTAGCCATTCGAA 59.054 41.667 5.39 0.00 0.00 3.71
2444 2978 5.299782 GCTACTGTAGTACTGTCTAGCCATT 59.700 44.000 15.27 0.00 30.33 3.16
2447 2981 3.565063 GGCTACTGTAGTACTGTCTAGCC 59.435 52.174 25.86 25.86 41.36 3.93
2454 2988 5.236047 CCGTAACTAGGCTACTGTAGTACTG 59.764 48.000 15.71 5.69 0.00 2.74
2455 2989 5.104735 ACCGTAACTAGGCTACTGTAGTACT 60.105 44.000 15.71 15.36 0.00 2.73
2456 2990 5.119694 ACCGTAACTAGGCTACTGTAGTAC 58.880 45.833 15.71 9.53 0.00 2.73
2465 2999 2.899256 ACCACAAACCGTAACTAGGCTA 59.101 45.455 0.00 0.00 0.00 3.93
2469 3003 6.367686 AGAAAAACCACAAACCGTAACTAG 57.632 37.500 0.00 0.00 0.00 2.57
2521 3055 4.950475 TGTATGAAAGGTGTTTTGTGGTGA 59.050 37.500 0.00 0.00 0.00 4.02
2522 3056 5.255710 TGTATGAAAGGTGTTTTGTGGTG 57.744 39.130 0.00 0.00 0.00 4.17
2527 3061 8.417780 TCAATTGTTGTATGAAAGGTGTTTTG 57.582 30.769 5.13 0.00 0.00 2.44
2532 3073 7.206981 ACTCTCAATTGTTGTATGAAAGGTG 57.793 36.000 5.13 0.00 0.00 4.00
2535 3076 9.734620 TTTGAACTCTCAATTGTTGTATGAAAG 57.265 29.630 5.13 0.00 41.22 2.62
2721 3285 8.945930 CAAATTGCAAATTGTTCATTGTGTTAC 58.054 29.630 17.40 0.00 0.00 2.50
2723 3287 6.472808 GCAAATTGCAAATTGTTCATTGTGTT 59.527 30.769 24.27 0.00 44.26 3.32
2725 3289 6.427300 GCAAATTGCAAATTGTTCATTGTG 57.573 33.333 24.27 3.28 44.26 3.33



Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.